[gmx-users] re: ciis peptide linkage

Justin A. Lemkul jalemkul at vt.edu
Fri May 20 22:09:47 CEST 2011

Frank Neuhaus wrote:
> Hello,
> In the process of simulating my protein, I find three residues that 
> don't "behave"  Notes indicate an unusual bond.  I am finding out that 
> the peptide bonds in the fragment containing these residues are linked 
> by cis-peptide linkages.  Does Gromacs have difficulty with the rare cis 
> peptide bond in a protein?   It reports "unusual bond between e.g. 
> 193(protein) and 194(none) and the VMD viewer places the residue to the 
> side of the box.  Any thoughts?

VMD only guesses where it thinks bonds should be based on distance cutoffs.  The 
only true bonds are in the topology, of which VMD is completely unaware.  Take 
the warnings with a grain of salt.

The geometry of peptide bonds is enforced by dihedrals, both proper and 
improper, and different geometries may or may not be parameterized in different 
force fields, although I suspect most deal with only the trans form.  If there 
are some weird transitions occurring, then perhaps the topology is broken, 
although if it was produced by pdb2gmx, then this is highly unlikely.  Incorrect 
.mdp settings could produce unphysical behavior, as well, such that the 
simulation is only metastable - it runs but produces strange output.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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